Advertisement

Evolutionary Design of a DDPD Model of Ligation

  • Mark A. Bedau
  • Andrew Buchanan
  • Gianluca Gazzola
  • Martin Hanczyc
  • Thomas Maeke
  • John McCaskill
  • Irene Poli
  • Norman H. Packard
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3871)

Abstract

Ligation is a form of chemical self-assembly that involves dynamic formation of strong covalent bonds in the presence of weak associative forces. We study an extremely simple form of ligation by means of a dissipative particle dynamics (DPD) model extended to include the dynamic making and breaking of strong bonds, which we term dynamically bonding dissipative particle dynamics (DDPD). Then we use a chemical genetic algorithm (CGA) to optimize the model’s parameters to achieve a limited form of ligation of trimers—a proof of principle for the evolutionary design of self-assembling chemical systems.

Keywords

Strong Bond Chemical System Dissipative Particle Dynamic Random Force Evolutionary Design 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Tuerk, C., Gold, L.: Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505–510 (1990)CrossRefGoogle Scholar
  2. 2.
    Ellington, A.D., Szostak, J.W.: In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990)CrossRefGoogle Scholar
  3. 3.
    Irvine, D., Tuerk, C., Gold, L.: SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. Journal of Molecular Biology 222, 739–761 (1991)CrossRefGoogle Scholar
  4. 4.
    Chapman, K.B., Szostak, J.W.: In vitro selection of catalytic RNAs. Current Opinions in Structural Biology 4, 618–622 (1994)CrossRefGoogle Scholar
  5. 5.
    Rohatgi, R., Bartel, D.P., Szostak, J.W.: Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3’-5’ phosphodiester bonds. Journal of the American Chemical Society 118, 3340–3344 (1996)CrossRefGoogle Scholar
  6. 6.
    Wright, M., Joyce, G.: Continuous in vitro evolution of catalytic function. Science 276, 614–617 (1997)CrossRefGoogle Scholar
  7. 7.
    Joyce, G.: Directed evolution of nucleic acid enzymes. Annual Review of Biochemistry 73, 791–836 (2004)CrossRefGoogle Scholar
  8. 8.
    Rasmussen, S., Chen, L., Deamer, D., Krakauer, D., Packard, N., Stadler, P., Bedau, M.: Transitions from nonliving to living matter. Science 303, 963–965 (2004)CrossRefGoogle Scholar
  9. 9.
    Joyce, G.F., Inoue, T., Orgel, L.E.: Non-enzymatic template-directed synthesis on RNA random copolymers. Poly(C, U) templates 176, 279–306 (1984)Google Scholar
  10. 10.
    Acevedo, O.L., Orgel, L.E.: Non-enzymatic transcription of an oligodeoxynucleotide 14 residues long. Journal of Molecular Biology 197, 187–193 (1987)CrossRefGoogle Scholar
  11. 11.
    Zielinski, W.S., Orgel, L.E.: Oligoaminonucleoside phosphoramidates. Oligomerization of dimers of 3’-amino-3’-deoxy-nucleotides (GC and CG) in aqueous solution. Nucleic Acids Research 15, 1699–1715 (1987)CrossRefGoogle Scholar
  12. 12.
    Joyce, G.F., Orgel, L.E.: Non-enzymatic template-directed synthesis on RNA random copolymers. Poly(C,A) templates. Journal of Molecular Biology 202, 677–681 (1988)CrossRefGoogle Scholar
  13. 13.
    Hill Jr., A.R., Orgel, L.E., Wu, T.: The limits of template-directed synthesis with nucleoside-5’-phosphoro(2-methyl)imidazolides. Origins of Life and Evolution of the Biosphere 23, 285–290 (1993)CrossRefGoogle Scholar
  14. 14.
    Liu, R., Orgel, L.E.: Enzymatic synthesis of polymers containing nicotinamide mononucleotide. Nucleic Acids Research 23, 3742–3749 (1995)CrossRefGoogle Scholar
  15. 15.
    Bohler, C., Nielsen, P.E., Orgel, L.E.: Template switching between PNA and RNA oligonucleotides. Nature 376, 578–581 (1995)CrossRefGoogle Scholar
  16. 16.
    Hoogerbrugge, P., Koelman, J.: Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhysics Letters 19, 155–160 (1992)CrossRefGoogle Scholar
  17. 17.
    Groot, R., Warren, P.: Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulations. Journal of Chemical Physics 107, 4423–4435 (1997)CrossRefGoogle Scholar
  18. 18.
    Marsh, C.: Theoretical aspects of dissipative particle dynamics. Ph.D. Thesis, University of Oxford (1998)Google Scholar
  19. 19.
    Shillcock, J., Lipowsky, R.: Equilibrium structure and lateral stress distribution from dissipative particle dynamics simulations. Journal of Chemical Physics 117, 5048–5061 (2002)CrossRefGoogle Scholar
  20. 20.
    Vattulainen, I., Karttunen, M., Besold, G., Polson, J.: Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models. Journal of Chemical Physics 116, 3967–3979 (2002)CrossRefGoogle Scholar
  21. 21.
    Trofimov, S., Nies, E., Michels, M.: Thermodynamic consistency in dissipative particle dynamics simulations of strongly nonideal liquids and liquid mixtures. Journal of Chemical Physics 117, 9383–9394 (2002)CrossRefGoogle Scholar
  22. 22.
    Jury, S., Bladon, P., Cates, M., Krishna, S., Hagen, M., Ruddock, N., Warren, P.: Simulation of amphiphilic mesophases using dissipative particle dynamics. Physical Chemistry and Chemical Physics 1, 2051–2056 (1999)CrossRefGoogle Scholar
  23. 23.
    Yamamoto, S., Maruyama, Y., Hyodo, S.: Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules. Journal of Chemical Physics 116, 5842–5849 (2002)CrossRefGoogle Scholar
  24. 24.
    Kranenburg, M., Venturoli, M., Smit, B.: Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics. Journal of Physical Chemistry 107, 11491–11501 (2003)CrossRefGoogle Scholar
  25. 25.
    Yamamoto, S., Hyodo, S.: Budding and fission dynamics of two-component vesicles. Journal of Chemical Physics 118, 7937–7943 (2003)CrossRefGoogle Scholar
  26. 26.
    von Kiedrowski, G.: A self-replicating hexadeoxynucleotide. Angewandte Chemie International Edition English 25, 932–935 (1986)CrossRefGoogle Scholar
  27. 27.
    Tjivikua, T., Ballester, P., Rebek, J.J.: A self-replicating system. Journal of the American Chemical Society 112, 1249–1250 (1990)CrossRefGoogle Scholar
  28. 28.
    Suzuki, H., Sawai, H.: Chemical genetic algorithms — Coevolution between codes and code translation. In: Standish, R.K., Bedau, M.A., Abbass, H.A. (eds.) Proceedings of the Eighth International Conference on Artificial Life (Artificial Life VIII), pp. 164–172 (2002)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Mark A. Bedau
    • 1
    • 2
    • 3
  • Andrew Buchanan
    • 1
    • 2
  • Gianluca Gazzola
    • 1
    • 2
  • Martin Hanczyc
    • 1
    • 2
  • Thomas Maeke
    • 2
    • 4
  • John McCaskill
    • 2
    • 4
  • Irene Poli
    • 2
    • 5
  • Norman H. Packard
    • 1
    • 2
  1. 1.Protolife S.r.l.Marghera, VeneziaItaly
  2. 2.European Center for Living TechnologyVeneziaItaly
  3. 3.Reed CollegePortlandUSA
  4. 4.Biomolecular Information Processing, Ruhr-Universitat BochumSankt AugustinGermany
  5. 5.University of Venice Ca’ FoscariVeneziaItaly

Personalised recommendations